Systems biology - model import

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Revision as of 11:41, 16 March 2022 by Elena Kutumova (Talk | contribs)

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To import SBML model, do the following:

  1. Find the folder in the BioUML repository where you want to download the model (for example, use the temporary folder in the tree: data/Collaboration/Demo/Data/Temp). Then, right-click on this folder and select "Import".

    Import model 01.png

  2. In the window that opens, click on the "Computer" button and find the document with the model in the file system of your computer.

    Import model 02.png

  3. Select the document and click on the "Start" button.

    Import model 03.png

  4. The model will appear in the BioUML repository and will be opened in a new workspace tab.

    Import model 04.png

Adjusting model layout

To change the default layout of the model, use the Layout tab in the right bottom panel.


Model layout 01.png

Currently, BioUML contains the folloing layout schemes:


Select the desired scheme and click on the Prepare layout button Execute icon.png. The newly generated layout will be shown on the right in the same tab.


Model layout 02.png

Then, click on the Apply layout button Add2docpane icon.png to apply this layout to the model diagram in the document pane.


Model layout 03.png

The selected layout scheme will apply to the model.


Model layout 04.png

Basic model editing

To edit any entity of the model, click on the corresponding element in the diagram and then click the Edit button Edit icon.png.


Systems biology egiting entities.png

The same actions can be performed for model reactions.


Systems biology egiting reactions.png

To edit model variables, use the Variables tab and after making changes, click the Save button Save icon.png to reflect these changes in the current version of the model.


Systems biology egiting parameters.png

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